Dear Martin,
I am not sure to fully understand (or understand the consequences)
mtmor...@fhcrc.org writes:
Bioconductor developers:
The Bioc release schedule is available
http://bioconductor.org/developers/release-schedule/
A reminder that version 2.13 of Bioconductor will be
Dear All,
Suppose a package contains a vignette that is built quickly
(small.Rnw) and another that takes a long time (big.Rnw).
We want to provide both the source and the PDF for both, but on routine
CMD build we only want to build the short one (the PDF for the long one
having been
As you describe this, this seems to be a change from the previously
documented (in R-exts) behaviour in R. Let us review the new
documentation and then we probably need to take it up with R-devel, but
before doing so, experience suggests that doing our homework is
beneficial. Is the package
I have reported this on R-devel. I think it is a bug or at least
unintended behavior.
If this does not get resolved, I would put the Rnw file inside /inst/Rnws
or some other directory. You don't (I assume) really care about the Rnw
file being installed, but you care about the PDF being present
Dear Kasper,
kasperdanielhan...@gmail.com writes:
Small complaints about the package: I am on OS X and first I have to deal
with the default of typedev on OS X to be the Cairo package which I don't
Actually, I started using Cairo because ADaCGH2 ought to be able to run in
headless servers
Actually, what I (and I think several others) just want is
fixSeqnames()
which sorts and fixes them to some convention. I don't really care which
one, but I want to do some easy harmonization, preferably in line with
other bioc tools. I know this is hard to do for all organisms, but having
Sounds great. Could we have a more intuitive name? Like naturalOrder(). And
then the method to fix the GRanges could be restoreNaturalOrder(). Just
some suggestions...
On Tue, Sep 17, 2013 at 10:58 AM, Hervé Pagès hpa...@fhcrc.org wrote:
For sorting the chromosome names in natural order, you
On 09/17/2013 11:30 AM, Michael Lawrence wrote:
Sounds great. Could we have a more intuitive name? Like naturalOrder().
That would be confusing because order() does something different:
order(c(chrY, chr1, chr9, chr2))
[1] 2 4 3 1
makeSeqnameIds(c(chrY, chr1, chr9, chr2))
[1] 4 1 3
I have been doing this in a kludgey fashion for a long long time, and would
favor restoreNaturalOrder() as a clear name for what it does. It would be
great to have this in BioC-2.13 release.
Thanks Michael and Herve and Kasper for bringing up and solving this cleanly.
--t
On Sep 17, 2013,
For sorting the chromosome names in natural order, you can use
the makeSeqnameIds() helper function in GenomicRanges:
seqlevels(gr) - seqlevels(gr)[makeSeqnameIds(seqlevels(gr))]
It recognizes several naming conventions (chr-prefixed or not,
roman, etc...) e.g.:
makeSeqnameIds(c(Y, 1, 9,
OK I just made sortSeqlevels() a generic with a method for character
vectors and a default method. So you can do sortSeqlevels() directly on
a Seqinfo object, a GRanges object and anything that contains a Seqinfo
component:
gr
GRanges with 0 ranges and 0 metadata columns:
seqnames
On 09/17/2013 10:58 AM, Hervé Pagès wrote:
For sorting the chromosome names in natural order, you can use
the makeSeqnameIds() helper function in GenomicRanges:
seqlevels(gr) - seqlevels(gr)[makeSeqnameIds(seqlevels(gr))]
I meant:
seqlevels(gr) -
Thanks, Hervé, that's great.
Would it make sense to have a sort or sortSeqlevels method for Seqinfo and
then a sortSeqlevels,ANY method that just does seqinfo(x) -
sort(seqinfo(x))?
Michael
On Tue, Sep 17, 2013 at 12:56 PM, Hervé Pagès hpa...@fhcrc.org wrote:
On 09/17/2013 10:58 AM, Hervé
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